Tip #1: Make your copies 1x per week.
I make all my copies for the coming week, on the Monday of every week. This allows me to organize everything for the week before we get too deep into it and I have other things to do. If you don't have time Monday morning, I suggest you stay late on Friday afternoon [when everyone else is itching to leave] and make your copies for the following week then. That's actually a great idea because you'll probably have the copier to yourself ;)
Tip #2: Have a designated location
I keep everything for a certain unit, in a binder; I mean everything. When I make copies, I hole-punch them, and they go in the binder, right in front of the original [which is in a sheet protector so I never give out the original]. By keeping them in the binder, I NEVER lose them :) I also don't have to remember where I put it for each class, or where I put extras if a kid needs another one...it's in the binder.
If you'd really like to cut down on your copy load, you can do one of two things. First, you can make one copy for each class, and put it up under the document camera, and the kids can write the info on their own notebook paper. This make add time to your activity because you're waiting for kids to copy it down, but you've saved your after-school copy time. Second, you can put the handout on your teacher website/page, and students can pull it up in class to look at it. We are fortunate to have a computer cart in each room with 30 Chrome-books. So if I need the kids to read an article and then write an analysis, instead of printing 100 copies of the article, I can put it on my wiki and the kids can read it there. Now, this doesn't allow for annotation, but that's a choice you can make.
Hope these little tips helped when it comes to organizing your copies. Let me know if you have any other ideas!! Feel free to share below in the comments for us all to see :)